NOC3L
protein-codingNOC3 like DNA replication regulator, the group of Armadillo like helical domain containing
Gene summary
Enables RNA binding activity. Predicted to be involved in DNA replication initiation. Predicted to act upstream of or within fat cell differentiation. Located in nucleolus and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]
- C10orf117
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~29.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to NOC3L variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_022451.11. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 98 | 1 | 99 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 0 | 104 | 1 | 0 | 105 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_071896.8 | 21 | MANE Select | |
| Ensembl | ENSP00000360412.3 | 21 | MANE Select | |
| Ensembl | ENSP00000522476.1 | 21 | Standard | |
| Ensembl | ENSP00000522476.1 | 21 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| noc3l | Danio rerio | Structure: neutrophil Quality: decreased amount abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- regulation of transcription by RNA polymerase II
- fat cell differentiation
Molecular Function
- DNA-binding transcription factor activity, RNA polymerase II-specific
- chromatin binding
- RNA binding
Cellular Component
- nucleus
- nucleolus
- mitochondrion
- nuclear speck
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000371361
- Coding exons
- 21
- Length
- 47713
- Individuals with no LoFs
- 125397
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 351
- Defined
- 125748
- p
- 0.00140
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.446 | 371 | 396 | 0.937 | 0.0000193 | 5249 |
| Missense (PolyPhen) | 90 | 108.95 | 0.82609 | 1449 | ||
| Synonymous | -0.107 | 136 | 134 | 1.01 | 0.00000621 | 1438 |
| Loss of Function | 2.34 | 29 | 46.1 | 0.629 | 0.00000250 | 588 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00074 | 0.00074 | rare |
| Latino/Admixed American | 0.00033 | 0.00032 | rare |
| Ashkenazi Jewish | 0.00030 | 0.00030 | rare |
| East Asian | 0.00085 | 0.00082 | rare |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.0024 | 0.0023 | notable |
| South Asian | 0.0010 | 0.0010 | notable |
| Other | 0.0015 | 0.0015 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May be required for adipogenesis. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.0981
Intolerance Scores
- LoFtool
- 0.952
- RVIS EVS
- 2.14
- RVIS percentile EVS
- 97.95
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- N
- Indispensability score
- 0.312
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | Medium | High |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |